cd07-0-Mosaic-class: Class "Mosaic"

In ClassDiscovery: Classes and Methods for "Class Discovery" with Microarrays or Proteomics

Description

Produce “Eisen” plots of microarray or proteomics data.

Usage

Mosaic(data,
       sampleMetric="pearson",
       sampleLinkage="average",
       geneMetric="euclid",
       geneLinkage="average",
       usecor=FALSE,
       center=FALSE,
       name="My mosaic")
## S4 method for signature 'Mosaic'
pltree(x, colors, labels, ...)
## S4 method for signature 'Mosaic,missing'
plot(x, main=x@name, center=FALSE,
  scale=c("none", "row", "column"), limits=NULL,
  sampleColors=NULL, sampleClasses=NULL,
  geneColors=NULL, geneClasses=NULL, ...)

Arguments

data	Either a data frame or matrix with numeric values or an ExpressionSet as defined in the BioConductor tools for analyzing microarray data.
sampleMetric	Any valid distance metric that can be passed to the distanceMatrix function
sampleLinkage	Any valid linkage method that can be passed to the hclust function
geneMetric	Any valid distance metric that can be passed to the distanceMatrix function
geneLinkage	Any valid linkage method that can be passed to the hclust function
center	logical scalar. If TRUE, center the data rows.
usecor	logical scalar. If TRUE, scale the data rows to have standard deviation one.
name	character string specifying the name of this object
x	object of class Mosaic
scale	Same as in heatmap.
colors	An optional vector of character strings containing color names to be used when labeling the trees in the dendrogram. If provided, then the length should equal the number of columns in the original data matrix.
labels	An optional vector of character strings used to label the leaves in the dendrogram. If omitted, the column names are used.
main	character string specifying the main title for the plot
limits	An numeric vector. If provided, the data is truncated for display purposes, both above and below, at the minimum and maximum values of limits.
sampleColors	An optional character vector containing colors that will be used to label different sample types with a color bar across the top of the heat map.
sampleClasses	A logical vector or factor used to classify the samples into groups. Alternatively, an integer specifying the number k of groups into which to cut the sample dendrogram.
geneColors	An optional character vector containing colors that will be used to label different gene types with a color bar along the side of the heat map.
geneClasses	A logical vector or factor used to classify the genes into groups. Alternatively, an integer specifying the number k of groups into which to cut the gene dendrogram.
...	Additional parameters for heatmap.

Details

One of the earliest papers in the microarray literature used independent clustering of the genes (rows) and samples (columns) to produce dendrograms that were plotted along with a red-green heat map of the centered expression values. Since that time, literally thousand of additional papers have published variations on these red-green images. R includes a function, heatmap that builds such figures. However, that function is general purpose and has numerous optional parameters to tweak the display. The purpose of the Mosaic class is to provide a simplified object-oriented wrapper around heatmap, which as a side benefit allows us to keep track of the distance metrics and linkage rules that were used to produce the resulting figure.

Value

The Mosaic function constructs and returns a valid object of the Mosaic class.

Objects from the Class

Objects should be created with the Mosaic function.

Slots

data:

The matrix containing the numerical data

samples:

A dendrogram of class hclust produced by clustering the biological samples (columns of data).

genes:

A dendrogram of class hclust produced by clustering the genes (columns of data).

sampleMetric:

A character string; the distance metric used to cluster the samples.

sampleLinkage:

A character string; the linkage rule used to cluster the samples.

geneMetric:

A character string; the distance metric used to cluster the genes.

geneLinkage:

A character string; the linkage rule used to cluster the genes.

call:

An object of class call recording how the object was constructed.

name:

A character string; the name of this object.

Methods

plot

signature(x = Mosaic, y = missing): Produce the “Eisen” plot, using heatmap.

pltree

signature(x = Mosaic): Plot the sample class dendrogram in the object.

summary

signature(object = Mosaic): Write out a summary of the object.

Author(s)

Kevin R. Coombes [e-mail], P. Roebuck [e-mail]

References

Eisen MB, Spellman PT, Brown PO, Botstein D.
Cluster analysis and display of genome-wide expression patterns.
Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14863-8.

See Also

cutree, hclust, heatmap

Examples

showClass("Mosaic")

## simulate data from three different sample groups
d1 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
d2 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
d3 <- matrix(rnorm(100*10, rnorm(100, 0.5)), nrow=100, ncol=10, byrow=FALSE)
dd <- cbind(d1, d2, d3)
kind <- factor(rep(c('red', 'green', 'blue'), each=10))

## prepare the Mosaic object
m <- Mosaic(dd,
            sampleMetric='pearson',
            geneMetric='spearman',
            center=TRUE,
            usecor=TRUE)
summary(m)

## The default plot with red-green color map
plot(m, col=redgreen(64))

## change to a blue-yellow color map, and mark the four top splits in the
## sample direction with a color bar along the top
plot(m, col=blueyellow(128), sampleClasses=4,
     sampleColors=c('red', 'green', 'blue', 'black'))

## This time, mark the three classes that we know are there
plot(m, col=blueyellow(128), sampleClasses=kind,
     sampleColors=c('red', 'green', 'blue'))

plot(m, col=blueyellow(128),
     geneClasses=3, geneColors=c('red', 'green', 'black'))

## In addition, mark the top 5 splits in the gene dendrogram
plot(m,
     col=blueyellow(128),
     sampleClasses=kind,
     sampleColors=c('red', 'green', 'black'),
     geneClasses=5,
     geneColors=c('cyan', 'magenta', 'royalblue', 'darkgreen', 'orange'))

## plot the sample dendrogram by itself
cols <- as.character(kind)
pltree(m, labels=1:30, colors=cols)

## cleanup
rm(d1, d2, d3, dd, kind, cols, m)

Example output

Loading required package: cluster
Loading required package: oompaBase
Class "Mosaic" [package "ClassDiscovery"]

Slots:
                                                                            
Name:           data       samples         genes  sampleMetric sampleLinkage
Class:        matrix        hclust        hclust     character     character
                                                              
Name:     geneMetric   geneLinkage          call          name
Class:     character     character          call     character
My mosaic, an object of the Mosaic class.

Call:
	Mosaic(data = dd, sampleMetric = "pearson", geneMetric = "spearman", usecor = TRUE, center = TRUE)

Sample dendrogram constructed with "average" linkage and "pearson" distance metric.

Gene dendrogram constructed with "average" linkage and "spearman" distance metric.

ClassDiscovery documentation built on Aug. 4, 2021, 3 p.m.